A sztereoizoméria hatása peptidek térszerkezetére és bioaktivitására = The effect of stereoisomerism on the spatial structure and bioactivity of peptides

Kutatásom során tanulmányoztam a cisz-transz és L-D izomériának a peptidek térszerkezeti és konformációs tulajdonságaira, illetve bioaktivitására kifejtett hatásait. Az opioid peptidek összehasonlító konformáció-analízise alapján azonosítottam a sztereoizomerek karakterisztikus térszerkezeti sajátságait, illetve a peptidek közötti konformációs hasonlóságokat és különbségeket. A farmakofór elemek relatív térbeli elrendeződésének leírására használt módszer alkalmasnak bizonyult a sztereoizomerek egymástól való megkülönböztetésére, és a farmakofórok térbeli összefüggéseinek jellemzésére. Az antimikrobiális peptidek esetén meghatároztam a cisz-transz izomériának a sztereoizomerek konformációs tulajdonságainak kialakításában és a peptidek dinamikus viselkedésében betöltött szerepét. A bázikus aminosavakat tartalmazó alanin-alapú peptidekre vonatkozóan átfogóan feltérképeztük a folding folyamatokat, és a szimulációk alapján különböző módszerek alkalmazásával jellemeztük a hajtogatódási útvonalakat. Az antimikrobiális peptidek palindrom szekvenciái esetében elvégeztünk egy részletes térszerkezet-vizsgálatot, és azonosítottuk a peptidek jellegzetes térszerkezeti sajátságait. A peptid-micella/membrán rendszerek esetén tanulmányoztuk a sztereoizomer antimikrobiális peptidek micellához/membránhoz kötődésének folyamatát, illetve részletesen jellemeztük a sztereoizomerek micella- és membrán-kötött konformációit, valamint a peptidek és micellák/membránok között kialakuló kölcsönhatásokat. | In my project, the effects of cis-trans and L-D isomerisms on the structural and conformational properties, as well as on the bioactivity of peptides were studied. Based on the comparative conformational analysis of opioid peptides, the characteristic structural features of stereoisomers, as well as the conformational similarities and dissimilarities between the peptides were identified. The method, applied to describe the relative spatial arrangements of pharmacophore elements, proved to be suitable to distinguish the stereoisomers from one another, and to characterize the spatial relationships of pharmacophores. For the antimicrobial peptides, the role of cis-trans isomerism played in the formation of conformational properties of stereoisomers, and in the dynamic behaviour of peptides, was determined. The folding processes were comprehensively explored, regarding the alanine-based peptides containing basic amino acids, and based on the simulations, the folding pathways were characterized using various methods. A detailed structural investigation was performed on the palindromic sequences of antimicrobial peptides, and the typical structural features of peptides were identified. For the peptide-micelle/membrane systems, the binding processes of stereoisomeric antimicrobial peptides to micelle/membrane were studied, as well as the micelle- and membrane-bound conformations, and the interactions evolved between the peptides and micelles/membranes were characterized in detail

Discrimination between the Two Closely Related Species of the Operational Group B. amyloliquefaciens Based on Whole-Cell Fatty Acid Profiling

(1) Background: Bacillus velezensis and Bacillus amyloliquefaciens are closely related members of the “operational group B. amyloliquefaciens”, a taxonomical unit above species level within the ”Bacillus subtilis species complex”. They have similar morphological, physiological, biochemical, phenotypic, and phylogenetic characteristics. Thus, separating these two taxa from each another has proven to be difficult to implement and could not be pushed easily into the line of routine analyses. (2) Methods: The aim of this study was to determine whether whole FAME profiling could be used to distinguish between these two species, using both type strains and environmental isolates. Initially, the classification was determined by partial sequences of the gyrA and rpoB genes and the classified isolates and type strains were considered as samples to develop the identification method, based on FAME profiles. (3) Results: The dissimilarities in 16:0, 17:0 iso, and 17:0 FA components have drawn a distinction between the two species and minor differences in FA 14:0, 15:0 iso, and 16:0 iso were also visible. The statistical analysis of the FA profiles confirmed that the two taxa can be distinguished into two separate groups, where the isolates are identified without misreading. (4) Conclusions: Our study proposes that the developed easy and fast-automated identification tool based on cellular FA profiles can be routinely applied to distinguish B. velezensis and B. amyloliquefaciens

Studying the Helical Conformations of Aspereline Peptides

Asperelines are short-sequence peptaibol molecules, and these peptides composed of 10 residues were isolated from the Trichoderma asperellum. In our study, a detailed structural characterization was performed on the asperelines by means of molecular dynamics methods. For the aspereline peptides, the occurrence of various secondary structural elements (i.e. beta-turns and helical structures) was investigated along their entire sequences. The results derived from the simulated annealing calculations led to the observations that in the case of asperelines, the types I, III and III' beta-turn structures, as well as their stabilizing i <- i+3 H-bonds appeared. However, beside the different beta-turns, shorter or longer helical structures were also detected. Based on the results obtained by the molecular dynamics simulations, it was concluded that the three-dimensional structure of aspereline peptides could be characterized by helical conformations (i.e. 3(10)- and alpha-helix). Nevertheless, on the basis of individual molecular dynamics trajectories, it was observed that the asperelines could adopt not only the right-handed, but also the left-handed helical structures

Structural characterization of the short peptaibols trichobrachins by molecular-dynamics methods

A structural characterization was carried out by molecular-dynamics methods for eight trichobrachin peptides, to identify the conformational features of these short peptaibols. For all peptides, the backbone and side-chain conformations were investigated, different secondary structures, such as type-I and -III bturns as well as b-bend ribbon spirals, were determined in certain tetrapeptide units of the molecules, and the preferred rotamers of the side chains of amino acids were identified. Furthermore, the end-to-end and residue-residue distances were examined, as well as the fluctuations of backbone atoms were studied. Based on these results, the peptides were compared to one another. Our theoretical study indicated that trichobrachins could be characterized by typical structural properties, and both conformational similarities and dissimilarities were observed between these peptaibols. In summary, this structural investigation supplied a characterization of the various conformational features of eight trichobrachin peptides